Capture-Seq is a targeted next-generation sequencing (NGS) platform for characterizing between 1,000 and 450,000+ targets in any species (including complex polyploids).

Samples may be comprised of a single species, a mix of closely related species or distantly related taxa.

Capture-Seq is suitable for both high and low volume applications. There is no minimum sample number required to utilize an existing marker assay or for custom assay design.

Full-service pipeline

  • Validated panels available for agricultural & phylogenetic applications.
  • Tissue/DNA to FASTQ data & SNPs
  • Up to 5-week turnaround times

Superior Flexibility & Quality

  • Custom panels easily developed vs chip-based genotyping arrays
  • Less missing data than restriction enzyme genotyping-by-sequencing (GBS)

Suitable for:

  • Pre-breeding marker discovery
  • Plant & animal breeding & research
  • Phylogenetic analysis


Capture-Seq works with complex polyploids, broad ranges of taxa, and complex host/pathogen sample types.

Capture-Seq probes can be utilized for:

  • Genomic selection
  • Marker-assisted selection (MAS)
  • Genome-wide association studies (GWAS)
  • Marker identification
    • Single nucleotide polymorphisms (SNPs)
    • InDels
  • Exome Sequencing
  • QTL mapping
  • Transgene insertion characterization
  • Phylogenetic Analysis
    • Anchored Hybrid Enrichment
    • Ultra-Conserved Elements (UCEs)

Capture-Seq Technology

View Full Diagram

Capture-Seq vs Arrays & GBS

Genotyping SystemTargeted Genotyping DataData Interval per TargetDevelopment CostEase of Customization & AdaptationMissing Data %Ascertainment BiasRead Depth at Targets (Equivalent Sequencing)RepeatabilitySuitable for Novel Marker DiscoverySuitable for Haplotype REconstructionEase if Copy Number & Dosage DetectionAnalytical Complexity
Capture-SeqYes400-500bpLowHighLowLowPredictable & ControllableHighYesYesHighLow
Chip-Based ArraysYes1bpHighLowLowHighN/AHighNoNoLowLow
RADSeq/GBSNo90bpLowVery LowHighN/AOften LowLowYesYesLowHigh

Designed for discovery

Capture-Seq delivers data both within a target region and in the adjacent regions.  During sample preparation, genomic DNA is randomly fragmented (1), resulting in the target region being in the left, middle, and right of different fragments from the many genome copies within each sample.

After Capture-Seq probes hybridize to their target regions (2), during next-generation sequencing the molecules are sequenced in full. This results in sequence data obtained in the bordering / flanking regions (3).

Sequence depth is always greatest in the probe region for marker discovery and sequence characterization, with additional results discovered in the nearby regions.



Project Scope
Research goals & timelines
Species/group & sample volume


Capture-Seq probe synthesis
Predesigned or custom
Batch submissions or all-at-once


FASTQ data or assembled loci

Get Started Today